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#Geneious prime tutorial how to#
#Geneious prime tutorial software#

The highlighted restriction sites and indicated methylation eﬀect takes into consideration the neighboring sequence. Methylated restriction sites where cleavage has not been experimentally validated, or might be methylated but have ambiguities in the target sequence, are highlighted with an asterisk but not greyed out. Restriction sites are greyed out and marked with an asterisk if the ability of the restriction enzyme to cleave at the restriction site is variable, impaired or blocked (see Figure 14.1 Will not cleave when overlapping site is methylatedīlocked by methylation of the overlapping site in some but not all ﬂanking DNA contextsĬonﬂicting reports of sensitivity to methylation at the overlapping siteĮﬀects of methylation at the overlapping site have not been tested

Rate of cleavage is lower than for unmethylated overlapping site Not sensitive to methylation at the overlapping site To ﬁnd enzymes that do not cut a particular sequence, use Find non-cutting enzymes under the Cloning menu. To select the region between two cut sites on a sequence, Shift+click on the two restriction site annotations in the sequence view.

#Geneious prime tutorial software#

csv ﬁles for subsequent processing with other software such as e.g. Once the document is saved, two new tabs will appear above the sequence view: Enzymes displays the list of enzymes and their cut positions Fragments displays a list of fragments that would be produced from the restriction digests. If Highlight Methylation Sites is selected, restriction sites which would not be cleaved due to the presence of methylation by Dam, Dcm or EcoKI are greyed out and marked with an asterisk (for further information on Highlight Methylation Sites see below). The annotation shows the enzyme’s recognition site, cut site and methylation sensitivity. You can click on the column headers to sort the table ascending or descending by that column, and you can Shift+click and Ctrl+click to select a range of rows and to toggle the selection of a row, respectively.įigure 14.1: Find Restriction Sites restriction enzymes table accessible under the Advanced option.Īfter conﬁguring your options, click Apply to record the restriction enzyme site annotations on the sequence. Only the enzymes selected in this table will be considered in the analysis initially, all rows are selected. Advanced: This displays a table of all enzymes in your candidate set, including their recognition site, overhang, eﬀective length and methylation information (Figure 14.1.Must not cut between: Returns enzymes which only cut outside the speciﬁed bases.Must cut between (may cut outside): Returns enzymes which cut between the speciﬁed bases, and may also cut outside that region.Must only cut between: Returns enzymes which only cut between the speciﬁed bases.It is not possible to select a subregion with this setting. Cut Anywhere: Returns enzymes which cut anywhere in the entire sequence.If you have selected a region of sequence in the sequence viewer, clicking the refresh arrow next to the base number counters will copy the selected region to this setting. Specifying cut regions: To specify a region of sequence where you want the enzyme to cut or not cut, choose one of the options below, and use the base counters to specify a sequence range that the options apply to.If you set X to be 0, when this operation is complete, it will report which candidate enzymes do not cut the sequence.

Results for enzymes that cut the sequence more or less than this will be discarded. Enzymes must match X to Y times: only returns restriction enzymes which cut the sequence X to Y times.To select speciﬁc enzymes from a particular enzyme set, click the Advanced button (see below).

#Geneious prime tutorial how to#

If you have created your own restriction enzyme set from your local database then this will also be listed (see section 14.3įor how to create such a document). This includes the options to use commonly used, or all known commercially available restriction enzymes.

Candidate Enzymes lets you select a set of restriction enzymes from which you want to draw the ones to use in the analysis.

under the Tools → Cloning menu or open the Restriction Analysis tab to the right of the sequence viewer. To ﬁnd and annotate restriction sites on a nucleotide sequence, go to Find Restriction Sites.